I had the same problem - shifting from 1st to 2nd was very rough (much rougher than all other gear shifts) and always resulted in a CLUNK or CLANK or whatever.
At first, I spent some time adjusting the clutch tension, didn't help
Then I found if I up-shifted at the EXACT time I pulled in the clutch (not clutch then shift, but both as the same motion) it was much much smoother. I was thinking too much slack in the chain or something ?
Then I changed to full synthetic oil and that helped a little.
Then the strangest thing happened... I was adjusting my bike ergonomics for a long trip for some extra comfort and adjusted the shifting lever down a couple of notches to account for my long legs, and as soon as I did - smooth shifting - bizarre.
1) the angle of the torque changed enough to change how the gears shifted (probably not, but who knows)
2) the synthetic oil only had about 100 miles on it before I adjusted the shifter and it took a bit to fully smooth out (I did a couple 400+ mile days before I fully realized my 1-2 shift was much smoother).
3) the adjusted position of the shift lever was a more natural position for my foot and caused me to get a more "assertive" shift motion and made it so I am not shifting like an 8 year old girl anymore